The Prodigal Son
by Naruto the invincible
Summary: Kushina abandons Naruto after the kyubi is sealed in him.  Naruto is the first jinchuriki of kyubi.  What changes will this bring to Naruto's life.  First fanfic.  Please read and review.
1. Chapter 1

**THE PRODIGAL SON**

A/N: AU. Naruto is the first jinchuriki of the kyubi. The reasons for kyubi's attack will be explained later. Epic in length. Alive Kushina.

**Prologue: The Demon**

Kushina Uzumaki watched the child she had sired and named Naruto change before her very eyes as six whisker marks appeared on his cheeks and could not stop the gasp escaping her. That was only the beginning however. The infant's deep blue eyes changed color and became a very dark brown, almost black and his canines lengthened before her very eyes, the whole process causing the infant to cry at the top of his voice. Kushina could no longer contain her horror and she wailed.

**Kushina POV**

'This abomination, this, this demon could not be her child. This was the demon, who had killed her love, her husband and her Naruto both.' This was not her child. This was the kyubi incarnate.'

**Line break**

When Hiruzen Sarutobi finally came to the site of the battle a couple of kilometers away from Konoha, he came to a sight that would haunt him for the rest of his life. Minato Namikaze, his successor, was lying lifeless with the body of an infant by his side with markings of a seal clear on the infant's stomach. The said infant was crying as if in pain and when he eventually touched the infant, the boy was burning with fever. What was more disconcerting however was that Kushina Uzumaki, the wife of the Yondaime, was wailing her heart out. He would eventually get the whole story out of her and would find out that her child, Naruto had been killed by the kyubi along with the Yondaime, Naruto's body burnt to ashes, and that the child was the kyubi.

For Kushina Uzumaki, her son died the day of the kyubi attack. She would eventually come over her nightmares, strongwilled that she was.

When the Sandaime dropped the infant at the orphanage, he was asked for a name, and he inadvertently blurted Naruto.

Thus began the life of Naruto, the jinchuriki of kyubi.


	2. Chapter 2

**A/N: I forgot to mention in the prologue, but since it seems to be a tradition, here goes.**

**I do not own Naruto, any of the original characters or jutsus.**

**Mzr90**: Thanks for the review. I appreciate your suggestions. Don't worry, there won't be any incest and Naruto will be smart. As to whether he becomes a missing nin or not and hates Konoha or not, you will just have to read further.

**Gozlid**: Thanks for the review. Kushina is OOC and I can't just remove her from the story. I know its only 380 words, but it took me some time to unjumble them from my mind and write, so she stays. I hope you read further despite your reservation and warm up to the story. (Author's rant: Come on, unrealistic, really, dude/gal, this is **FANFICTION**, everything here is unrealistic.)

**Chapter 1: Damage Control, The Missing Biju, and War**

**Konoha: Two days later**

The reinstated Sandaime couldn't stop the sigh that escaped his lips as he looked at Naruto. The grapevine that was Konoha was ripe with rumors and he had already heard whispers with statements such as "the fox brat", "the kyubi reborn" doing rounds as he wandered through the village trying to assess the situation. He had no doubt that news of Kyubi's attack and the new jinchuriki would reach the ears of Konoha's allies as well as enemies. While that was a good thing on the one side as it would serve as a deterrent for war, on the other he had not only heard the stories of jinchuriki's treatments, he had seen it firsthand as well. It was a brutal picture and he was already beginning to see the picture's first few strokes in Konoha.

He shook himself out of the apathy and went into his Hokage mode. He went through various options coursing through his mind and came to a decision. Flaring his chakra, he waited for the anbu to come. It was Neko.

"Neko."

"Hai, Hokage sama."

"Every citizen and shinobi of Konoha is to gather on the ground within 2 hours."

"Hai, Hokage sama."

**Three hours later**

**With Danzo**

Danzo shook his head as a wry chuckle escaped his lips. His moment was close, he could feel it in his bones. He had waited patiently for Hiruzen to make a mistake, and what a wait it had been. It had been almost 50 years since Hiruzen became Hokage the first time. Whatever mistakes Hiruzen had made before he retired, they were minor, mistakes he had to acknowledge he could have made himself, but whatever problems these mistakes had created were squashed in the bud, either by the Hokage himself or by the Root. Hiruzen, however, had retired. For whatever reasons, the Sandaime was nowhere near his prime when he retired after the third shinobi world war. He was both mentally and physically tired, his will of fire dimmed. And now he was thrust back into a job he had vacated himself because he found himself unfit to do it anymore. He was mentally unprepared for the sudden responsibility and he had made the mistake of antagonizing his people. Hiruzen was weak now. It would need just a few more pushes and Konoha would be his, the first step towards the domination of the Elemental Nations.

**With Hiruzen Sarutobi**

He had made a mistake. He knew it as soon as he lay down the law and saw his people's response.

"No one under the rank of jonin for the shinobi and the age of 18 for the civilians, who already don't know, are to know of Naruto's status. If anyone even speaks of the kyubi or Naruto in the same breath to anyone, it will mean treason, and the person will be executed on the spot."

There was an uproar. He did not expect this. His attempt at damage control had backfired heavily. Almost a riot had started and had the anbu not put two civilians to death then and there it certainly would have. The crowd quietened down. They would follow the Sandaime's law, but the incident would leave a mark in the civilian's psyche. The shinobi used to bloodshed and accepting the authority of Hokage looked at this as if it were routine. They also understood that the jinchuriki would be their trump card when push came to shove, besides the law was laid down and the civilians should have known better.

Hiruzen Sarutobi paced in his office knowing he had made a grave mistake. Trying to protect this child from the life a jinchuriki usually suffered had made him antagonize at best only a few civilians and at worst a majority of his people, civilians and shinobi alike, who had lost their loved ones to kyubi. He was not prepared for the job and he had made a grave mistake, the likes of which Danzo wouldn't hesitate to capitalize on. Any help he gave the child now would have to be kept secret from the council. That limited his options severely, but he could not and most certainly would not let Konoha fall into hands of warmongers like Danzo just so he could give the child a better life. Naruto's life would be hard, he knew, but he had to give this sacrifice for Konoha.

The Sandaime would burn midnight oil that night deciding what to do with Naruto before going to sleep.

**Somewhere underground in Kirigakure**

Madara Uchiha could not stop the laughter. He was cackling madly, insanity shining through his eyes. It was out of character for the silent Uchiha, any Uchiha for that matter, to laugh with such free abandon, but he just couldn't control himself. The kyubi had attacked Konoha and while Konoha had lost their Yondaime, they had gained a jinchuriki.

Zetsu had never seen Madara like this and not able to keep curiosity out of his voice, he, or rather they, finally asked Madara the question on their mind.

"We have never seen you like this, Konoha is not destroyed you know."

Madara continued to laugh for a few more minutes, before he spoke, "I know. I am laughing at the irony of the situation. I have been searching for the kyubi for the last 20 years, the second Madara had searched for it since it disappeared after the first Madara's fight with the Senju. I am laughing because together we have searched for 100 years, give or take a few, and now it just pops up in Konoha and is sealed. It is amazing how little we actually do know about the biju. I am the one who knows most about the biju in all of the elemental nations, and I doubt I know 20% of it. You do know the supposed theory don't you?", Madara asked.

Zetsu nodded. "The theory says that when a biju dies or disappears into its world for whatever reasons, it takes double the number of years to its tails for it to reform."

"Indeed and yet I clearly remember that when the kyubi disappeared in the middle of the battle, it had only 2 tails left, meaning it should have reformed in 14 years, and yet it has almost taken 100 years for the kyubi to reform. I had almost given up hope like my predecessor."

"I don't get it," Zetsu said. "What do you mean search for it, why not summon it like the first?"

Madara sighed. "Only the first Madara had enough life force and chakra to summon the kyubi and make it fight for him. I had been searching for it in the realm the first Madara used to summon it from, but hadn't found it. No matter though, the final piece of the puzzle, the missing biju is finally in place. Soon I will hand over the reins to the fourth Madara and then we will capture all the jinchuriki. My vision has never failed me yet and it never will, ever. The world will be mine."

**Kumogakure**

The Kumogakure council was in deep contemplation as to the action to take about the news from Konoha. The Sandaime Raikage stood up and addressed the council.

"A biju attack is no joke. Kumo and Konoha were the strongest of the five after the third war. Iwa and Suna are economically struggling, Kiri is in chaos, and now with the biju attack Konoha is vulnerable; they have lost their strongest fighter and their jinchuriki is untrained. We all know what a trained jinchuriki can do and now they have the strongest biju. If Konoha is allowed to recover, they will train their jinchuriki and will once again be the strongest village. This won't do. Kumo stands to gain much if we defeat Konoha now before they have a chance to recover. We may even get some bloodlines as well as the jinchuriki of the kyubi. Kumo can very well dictate and decide the future."

The speech did it. War was coming to Konoha.


	3. Chapter 3

**Chapter 2: Konoha's Spymaster and Preparations for War**

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**One and a half months later**

Jiraya literally flew through the trees from across the border of the Fire Country towards Konoha. As soon as he got to a good enough clearing, he quickly pricked his finger and went through a few signs rapidly, before slamming the hand on the ground saying Kuchiyose no Jutsu (Summoning Technique), and a huge toad appeared in a puff of smoke. Jiraya climbed up the toad and soon they were bounding towards Konoha at unrivaled speeds.

As the toad did the traveling, Jiraya let his thoughts wander. What he had heard may or may not have been a rumor, but if they neglected this and it turned out to be true, then Konoha would be crushed, about that he was sure. The Sandaime Raikage was not a man to be trifled with, Jiraya knew. There were only a handful of people capable of taking on the Raikage, and there were only two in Konoha right now, he himself and his sensei, Hiruzen Sarutobi. He knew Konoha had to act quickly and hence he was making haste.

As soon as Konoha's gate was within site, he dispelled the toad and began running again, confident that the barrier he himself and his prized student, the Yondaime, had erected around Konoha would have recognized his chakra and alerted the guards and the Hokage himself by now. He ran through the gate without even acknowledging the chunin guarding the gates and made his way towards the Hokage tower.

**Hokage Tower—Hokage's Office**

"Jiraya, what's the matter?"

To say the Third Hokage was surprised was an understatement. In all his decades of interaction with Jiraya, he had only seen the man this grim on occasions he could count on one hand, and this did not bode well.

"Sensei, the rumor is that Kumo has ordered a large shipment of grains and other foodstuffs, as well as large quantities of ration bars. Also, shinobi cells in groups of twos and threes are slowly but surely moving towards our border. It is almost as if….." Jiraya left the sentence hanging.

But Hiruzen was not Hokage for nothing.

"They are preparing for a war." He said with finality. "Well done Jiraya. Stay for a bit now, I will call the War Council immediately."

**2 hours later**

**Hokage Tower—War Council**

All the clan heads, the Jonin Commander, the Anbu Head, as well as the most experienced Jonins were present along with the elder advisory Council. It was truly an illustrious Council and a walking advertisement of Konoha's Shinobi services. They were Tsume Inuzuka, Shikaku Nara, Inoichi Yamanaka, Chouza Akimichi, Hiashi Hyuga, Fugaku Uchiha, Shibi Aburame, Kakashi Hatake, Danzo Shimura, Koharu Utatane, Homura Mitokado, Jiraya of the Sannin, Kushina Uzumaki, and the Hokage himself, Hiruzen Sarutobi.

"And that's the situation." Jiraya finished.

It was Danzo who spoke up first.

"They have 2 well trained jinchuriki. Along with those two, the third Raikage and his son are the biggest threat. Right now the only people who can successfully defeat these 4 or at least draw with them are Jiraya, myself, Kushina San, and the Hokage himself. Jiraya and Kushina San are the most skilled amongst us in fuinjutsu as such it would be best if these two face the 2 jinchuriki. Myself and Hiruzen will handle the Raikage and his son."

"I hope we don't have to come to that." Said the Third Hokage. "Right now, our priority should be sabotage. I am sure that they eventually would want to bring all their supplies closer to the border right before the war begins. It would be in our best interests to do as much damage as we possibly can before going to war."

And so the discussions went on until the early morning hours. For now, Konoha's plan consisted of pure guerilla tactics. They would delay Kumo as long as they could while at the same time strengthening their defenses and getting ready for war. Jiraya would acquire information about the movement of shipments and supplies and Konoha's regular shinobies as well as Anbu would help destroy those, Jiraya would do the same should he get the chance. Meanwhile, the clan heads would increase their wards training to become more war oriented and the same would be done at the academy. At the same time, the Jonin Commander and the Anbu head would acquire all the supplies that this war entailed.

It was towards the end of the meeting the question was raised about Konoha's own jinchuriki. It was Danzo once again.

"What we need for the future is an army killer." Danzo said.

It was a statement not to be taken lightly. An army killer was simply a shinobi or a kunoichi who could on their own, with or without a jutsu, obliterate an army of five or more thousand shinobi.

"Right now, Konoha has 2, Jiraya and the Hokage himself." Danzo continued. "While myself and Kushina San aren't too far behind, we would probably kill ourselves in the effort. And myself and Hiruzen are advancing in years. In the future, we will need at least 1, possibly 2 or even 3 army killers in our ranks."

Suprisingly, it was Jonin Commander, Shikaku Nara, who responded. "Danzo San has a very valid point. While Konoha has remained strong through unparalleled teamwork, we have always had a few people with immense raw power or few with enough raw power and genius and cunning capable of working alone and destroying an army, and that is what we need again. And although a few of the next generation seem to have the genius, none of them have that raw power in them." Said Shikaku.

Danzo smirked mentally. Hiruzen may have kept Anbu on the jinchuriki round the clock, so that he could not get to him, but this war was the perfect excuse to harness the power of kyubi for Konoha's use he thought. It was time to bait.

"Except our own jinchuriki, he has the raw power, and given the right atmosphere, he can be taught to use that raw power." Danzo said.

There was pindrop silence in the council room as everyone digested just what Danzo had said. Before they had completed their thought process, however, he continued.

"Give the jinchuriki to me and by the time he is 6, he will be jonin level, by the time he is 8 Konoha can have one more army killer in its ranks." He hoped the council would take the bait. There were of course other ways of getting what he wanted, but the official way was not bad at all he mused.

Suprisingly, Kushina Uzumaki spoke for the first time since the meeting started.

"Giving him power will only cause harm to Konoha in the future. As soon as the monster was sealed in the child, the child changed, his hair color and his eyes are different than what he was born with and so are those whisker marks on his cheeks. Something went wrong with the sealing, those changes weren't supposed to happen." This was said in a clipped tone and with barely restrained anger, the hatred shining through her eyes.

"The seal is perfectly fine." It was Jiraya who spoke. "Kushina chan no one in Konoha was spared the Kyubi's wrath, but the child is no kyubi. I have gone over the seal myself and it is the strongest ever created to hold a biju, and it is holding strong as we speak. I checked it before coming here and there is no trace of demonic chakra. Your loss has made you blind Kushina chan, it is not the boy's fault." Said Jiraya kindly trying to calm Kushina, while at the same time making a point.

"I don't care for your expertise Jiraya. You don't outrank me as far as sealing is concerned. I am sorry Hokage Sama, but I must take my leave now." And she shunshinned out of the room, shocking everyone with her changed attitude. Kushina was kind and always smiling before Minato's death. Now, she had become broody and rude. And Jiraya was not only Minato's sensei, he was a father figure to Minato. To insult Jiraya showed the depths of despair she was in.

The Third Hokage spoke up before there were any more fireworks. "Danzo, even though you are right, I cannot give the jinchuriki to you to train. Don't worry though, Konoha will have one more army killer by the time I retire again. I have my own plans for the jinchuriki." And he adjourned the meeting leaving everyone to perform their assigned jobs.

**With Danzo**

Danzo sighed in defeat. The mistake Hiruzen had made in revealing the jinchuriki had made Danzo underestimate him and push him too far and there was no one who knew better than him how ferocious Hiruzen could be when his back was against the wall. This round went to Hiruzen, he thought, but by no means was the game over.

**Iwagakure—Tsuchikage's Office**

"Greetings Tsuchikage Sama."

"What's the news from Konoha."

"It is confirmed, Tsuchikage Sama. Even though Konoha has gained a new jinchuriki, the yellow flash is definitely dead."

"Good, take rest for a few days. You deserve it."

"There is more Tsuchikage Sama. Kumo is preparing for war. Fortunately, their troop movement is towards Konoha."

"Very well, you may go now."

This is perfect, thought Onoki. Kumo and Konoha, whoever weakens, Iwa will be there to take advantage and he bellowed for his Jonin Commander to call Iwa's own war council to discuss the upcoming war between Konoha and Kumo.

**Rice Country—A secret underground lab**

Orochimaru wondered how he could use this information. He had of course fought with a few jinchuriki in the Third Shinobi World War. They were a force to be reckoned with and now Konoha had one of their own and the strongest biju too. He had caught whispers of the Akatsuki wanting the jinchuriki for their own goals and he wondered if he could get and control the jinchuriki himself. Having one of the strongest jinchuriki act on your whims and fancy, now that would be orgasmic, he thought. He would have to plan for it. It was still too early to act, for he had defected not too long ago, and he still had to establish a strong base for himself in the rice country. But once that was done, yes, he thought, once that was done he would get for himself the jinchuriki and a few good specimens of the Sharingan.

Ku ku ku ku ku …..Orochimaru's evil laugh reverberated through the underground tunnel as he dreamt of ways to destroy Konoha with its own jinchuriki.

For now, Konoha's jinchuriki was the star attraction for all of the elemental nations.

**A/N: So just for review, now Akatsuki, Orochimaru, Kumo, Danzo, and even Hiruzen has plans for the kyubi jinchuriki. And Iwa seems to be waiting for the right opportunity to strike. I have explained when I plan to bring Naruto into picture again on my profile. It will probably be 4th or 5th chapter and from then on it will be all Naruto.**


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